19 |
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20 |
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#define BASE_SEED 123456789 |
21 |
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22 |
< |
Thermo::Thermo( SimInfo* the_entry_plug ) { |
23 |
< |
entry_plug = the_entry_plug; |
22 |
> |
Thermo::Thermo( SimInfo* the_info ) { |
23 |
> |
info = the_info; |
24 |
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int baseSeed = BASE_SEED; |
25 |
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|
26 |
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gaussStream = new gaussianSPRNG( baseSeed ); |
45 |
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Atom** atoms; |
46 |
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47 |
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48 |
< |
n_atoms = entry_plug->n_atoms; |
49 |
< |
atoms = entry_plug->atoms; |
48 |
> |
n_atoms = info->n_atoms; |
49 |
> |
atoms = info->atoms; |
50 |
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|
51 |
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kinetic = 0.0; |
52 |
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kinetic_global = 0.0; |
88 |
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int el, nSRI; |
89 |
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Molecule* molecules; |
90 |
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|
91 |
< |
molecules = entry_plug->molecules; |
92 |
< |
nSRI = entry_plug->n_SRI; |
91 |
> |
molecules = info->molecules; |
92 |
> |
nSRI = info->n_SRI; |
93 |
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|
94 |
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potential_local = 0.0; |
95 |
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potential = 0.0; |
96 |
< |
potential_local += entry_plug->lrPot; |
96 |
> |
potential_local += info->lrPot; |
97 |
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|
98 |
< |
for( el=0; el<entry_plug->n_mol; el++ ){ |
98 |
> |
for( el=0; el<info->n_mol; el++ ){ |
99 |
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potential_local += molecules[el].getPotential(); |
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} |
101 |
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129 |
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const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
130 |
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double temperature; |
131 |
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|
132 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
132 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
133 |
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return temperature; |
134 |
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} |
135 |
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151 |
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152 |
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double Thermo::getVolume() { |
153 |
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154 |
< |
return entry_plug->boxVol; |
154 |
> |
return info->boxVol; |
155 |
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} |
156 |
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157 |
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double Thermo::getPressure() { |
180 |
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double molmass, volume; |
181 |
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double vcom[3]; |
182 |
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double p_local[9], p_global[9]; |
183 |
< |
int i, j, k, l, nMols; |
183 |
> |
int i, j, k, nMols; |
184 |
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Molecule* molecules; |
185 |
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|
186 |
< |
nMols = entry_plug->n_mol; |
187 |
< |
molecules = entry_plug->molecules; |
188 |
< |
//tau = entry_plug->tau; |
186 |
> |
nMols = info->n_mol; |
187 |
> |
molecules = info->molecules; |
188 |
> |
//tau = info->tau; |
189 |
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|
190 |
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// use velocities of molecular centers of mass and molecular masses: |
191 |
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for (i=0; i < 9; i++) { |
222 |
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for(i = 0; i < 3; i++) { |
223 |
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for (j = 0; j < 3; j++) { |
224 |
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k = 3*i + j; |
225 |
< |
press[i][j] = (p_global[k] + entry_plug->tau[k]*e_convert) / volume; |
225 |
> |
press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
226 |
> |
|
227 |
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} |
228 |
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} |
229 |
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} |
245 |
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int n_oriented; |
246 |
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int n_constraints; |
247 |
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|
248 |
< |
atoms = entry_plug->atoms; |
249 |
< |
n_atoms = entry_plug->n_atoms; |
250 |
< |
temperature = entry_plug->target_temp; |
251 |
< |
n_oriented = entry_plug->n_oriented; |
252 |
< |
n_constraints = entry_plug->n_constraints; |
248 |
> |
atoms = info->atoms; |
249 |
> |
n_atoms = info->n_atoms; |
250 |
> |
temperature = info->target_temp; |
251 |
> |
n_oriented = info->n_oriented; |
252 |
> |
n_constraints = info->n_constraints; |
253 |
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|
254 |
< |
kebar = kb * temperature * (double)entry_plug->ndf / |
255 |
< |
( 2.0 * (double)entry_plug->ndfRaw ); |
254 |
> |
kebar = kb * temperature * (double)info->ndf / |
255 |
> |
( 2.0 * (double)info->ndfRaw ); |
256 |
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|
257 |
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for(vr = 0; vr < n_atoms; vr++){ |
258 |
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|
323 |
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// We are very careless here with the distinction between n_atoms and n_local |
324 |
|
// We should really fix this before someone pokes an eye out. |
325 |
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|
326 |
< |
n_atoms = entry_plug->n_atoms; |
327 |
< |
atoms = entry_plug->atoms; |
326 |
> |
n_atoms = info->n_atoms; |
327 |
> |
atoms = info->atoms; |
328 |
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|
329 |
|
mtot_local = 0.0; |
330 |
|
vdrift_local[0] = 0.0; |